cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXXMLFieldGetter.java

   1 package eu.etaxonomy.cdm.io.taxonx2013;
   2
   3 import java.net.URI;
   4 import java.util.ArrayList;
   5 import java.util.List;
   6 import java.util.Map;
   7
   8 import org.apache.log4j.Logger;
   9 import org.w3c.dom.Document;
  10 import org.w3c.dom.Node;
  11 import org.w3c.dom.NodeList;
  12
  13 import eu.etaxonomy.cdm.model.common.CdmBase;
  14 import eu.etaxonomy.cdm.model.description.Feature;
  15 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  16 import eu.etaxonomy.cdm.model.reference.Reference;
  17 import eu.etaxonomy.cdm.model.taxon.Classification;
  18
  19 public class TaxonXXMLFieldGetter {
  20
  21     private static final Logger logger = Logger.getLogger(TaxonXXMLFieldGetter.class);
  22     private final Document doc;
  23
  24
  25     private final NomenclaturalCode nomenclaturalCode;
  26     private Classification classification;
  27     private final TaxonXImport importer;
  28     private final TaxonXImportState taxonXstate;
  29     TaxonXModsExtractor modsextractor;
  30     TaxonXTreatmentExtractor treatmentextractor ;
  31
  32     public TaxonXXMLFieldGetter(TaxonXDataHolder dataholder, String prefix,Document document, TaxonXImport taxonXImport,
  33             TaxonXImportState taxonXstate, Classification classif, Map<String,Feature> featuresMap){
  34         this.doc = document;
  35         this.importer = taxonXImport;
  36         this.nomenclaturalCode = taxonXstate.getConfig().getNomenclaturalCode();
  37         this.classification = classif;
  38         logger.info("CLASSIFICATION "+classification);
  39         this.taxonXstate=taxonXstate;
  40         modsextractor = new TaxonXModsExtractor(importer);
  41         Reference<?> originalSourceUrl =taxonXstate.getConfig().getOriginalSourceURL();
  42         treatmentextractor = new TaxonXTreatmentExtractor(nomenclaturalCode,classification,importer, taxonXstate,featuresMap,originalSourceUrl );
  43     }
  44
  45
  46     /**
  47      * parse the Mods from the TaxonX file
  48      *
  49      *@return the created Reference object
  50      **/
  51     public Reference<?> parseMods(){
  52         //        System.out.println("PARSEMODS");
  53         //taxonx
  54         Node root = doc.getFirstChild();
  55
  56
  57         //taxonHeader, taxonBody
  58         NodeList nodes = root.getChildNodes();
  59         Reference<?> ref = null;
  60         for (int i=0; i< nodes.getLength();i++) {
  61             //            System.out.println(nodes.item(i).getNodeName());
  62             if (nodes.item(i).getNodeName().equalsIgnoreCase("tax:taxonxheader")){
  63                 NodeList nodes2 = nodes.item(i).getChildNodes();
  64                 for (int j=0; j< nodes2.getLength();j++){
  65                     //                    System.out.println("nodes2 : "+nodes2.item(j).getNodeName());
  66                     if (nodes2.item(j).getNodeName().equalsIgnoreCase("mods:mods")){
  67                         ref = modsextractor.extractMods(nodes2.item(j));
  68                         //                        System.out.println("reference: "+ref.getTitleCache());
  69                         importer.getReferenceService().saveOrUpdate(ref);
  70                         ref=CdmBase.deproxy(ref, Reference.class);
  71                     }
  72                 }
  73             }
  74         }
  75         if (ref!=null) {
  76             taxonXstate.getConfig().setClassificationName(ref.getCitation());
  77         } else {
  78             taxonXstate.getConfig().setClassificationName( "no reference title");
  79         }
  80         ref=CdmBase.deproxy(ref, Reference.class);
  81         return ref;
  82     }
  83
  84
  85     /**
  86      * Foreach treatment section, launches the treatment "extractor"
  87      * @param ref : the current reference, extracted from the mods
  88      * @param sourcename: the URI of the TaxonX document
  89      */
  90     public void parseTreatment(Reference<?> ref, URI sourceName){
  91         System.out.println("PARSETREATMENT "+ref);
  92         //taxonx
  93         Node root = doc.getFirstChild();
  94         //taxonHeader, taxonBody
  95         NodeList nodes = root.getChildNodes();
  96
  97         for ( int i=0; i< nodes.getLength();i++) {
  98             //            System.out.println(nodes.item(i).getNodeName());
  99             if (nodes.item(i).getNodeName().equalsIgnoreCase("tax:taxonxBody")){
 100                 NodeList nodes2 = nodes.item(i).getChildNodes();
 101                 for (int j=0; j< nodes2.getLength();j++){
 102                     if (nodes2.item(j).getNodeName().equalsIgnoreCase("tax:treatment")){
 103                         List<Object> tosave = new ArrayList<Object>();
 104                         treatmentextractor.extractTreatment(nodes2.item(j),tosave,ref,sourceName);
 105                     }
 106                 }
 107             }
 108         }
 109     }
 110
 111
 112
 113     /**
 114      * updates the classification in the treatment extractor
 115      * @param classification2
 116      */
 117     public void updateClassification(Classification classification2) {
 118         //System.out.println("UPDATECLASSIFICATIONS "+classification2);
 119         classification=classification2;
 120         if (treatmentextractor != null) {
 121             treatmentextractor.updateClassification(classification);
 122         }
 123
 124     }
 125
 126
 127     /**
 128      * @return
 129      */
 130     public Map<String,Feature> getFeaturesUsed() {
 131        return treatmentextractor.getFeaturesUsed();
 132     }
 133
 134
 135 }